A driver had a "miraculous escape" after his car and a train collided at one of the state's most dangerous level crossings.

Trains are running again after services on the Sunbury line between Sunshine and St Albans were suspended for hours on Thursday when the train crashed into the car as it was crossing the tracks at Furlong Road in Sunshine North.

Metro Trains announced shortly after 4pm that the line had reopened between Sunshine and Watergardens and delays of 10 minutes were expected as they caught up.

Earlier, an Ambulance Victoria spokeswoman said a man in his 20s had made a miraculous escape and had been transported to Western Hospital in Footscray with minor injuries.

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The four-door white SUV sustained heavy damage to its rear while the front end was crumpled by the impact of the crash, with the train pushing it into an adjacent traffic light and electricity pole.

VicRoads issued a statement advising all lanes of Furlong Road had reopened.

The Furlong Road crossing was ranked among the most dangerous in the state by the Department of Transport in 2008, with three people killed there in a single accident in 2004 and at least one other fatality 10 years earlier.

In October, 2011, 15-year-old Teresa Ho died when she was hit by V/Line train after she apparently failed to heed warning lights and alarms when she opened pedestrian gates at Ginifer railway station, just metres away from the road crossing. Witnesses reported she was listening to music at the time.

Despite passionate pleas from friends and family of victims, the state government at the time ruled out an urgent upgrade of the dangerous crossing.

Meanwhile, Metro has tweeted that there are delays on the Craigieburn line on Thursday evening because of a track fault.

"Metro work crews are on site working to fix the fault," Metro tweeted.